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Open data
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Basic information
Entry | Database: PDB / ID: 1npf | ||||||
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Title | MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRIC OXIDE | ||||||
![]() | Myoglobin![]() | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Copeland, D.M. / West, A.H. / Richter-Addo, G.B. | ||||||
![]() | ![]() Title: Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane. Authors: Copeland, D.M. / West, A.H. / Richter-Addo, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.9 KB | Display | ![]() |
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PDB format | ![]() | 31.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1npgC ![]() 1dwrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANIMAL OXYGEN STORAGE / Source: (natural) ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-HEM / | ![]() #4: Chemical | ChemComp-NO / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 23.76 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Method: vapor diffusion, hanging drop / pH: 7.4 Details: AMMONIUM SULFATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Chu, K., (2000) Nature, 403, 921. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 2002 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→40 Å / Num. obs: 17516 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 3.4 / % possible all: 91.1 |
Reflection | *PLUS Num. measured all: 34504 |
Reflection shell | *PLUS % possible obs: 91.1 % / Num. unique obs: 1687 / Num. measured obs: 3332 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1DWR Resolution: 1.9→40 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.021 /
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.384 / Rfactor Rwork: 0.365 |